[AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C

From: Morrow,John Kenneth <JKMorrow.mdanderson.org>
Date: Fri, 19 Jan 2018 23:14:12 +0000

I have been receiving the above error when trying to run MMPBSA. I searched the previous posts about this error, and have tried changing setting inp=1 and radiopt=0 in the &pb, but this does not solve the problem.

If I am reading the error correctly, the radius is not set for the 7th atom (CB atom) on the first residue in the structure, and I have tried multiple programs to prepare the protein (MOE, Pymol, Babel), and the atom/atom type does not seem to be atypical.

Input file for running PB and GB in serial:
   startframe=5, endframe=600, interval=10, keep_files=0,
                igb=5, saltcon=0.150
  istrng=0.15, fillratio=4.0

It returns with the following error:

Running calculations on normal system...

Beginning GB calculations with /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Beginning PB calculations with /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy
  calculating complex contribution...
  File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/MMPBSA.py", line 104, in <module>
  File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/opt/apps/intel16/cray_mpich_7_3/amber/14.0/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", line 431, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/apps/intel16/cray_mpich_7_3/amber/14.0/bin/mmpbsa_py_energy failed with prmtop /work/01936/jkmorrow/2nd.try_DS.and.Babel/com.top!
                PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C

Exiting. All files have been retained.

Any other suggestions to resolve this issue would be greatly appreciated, thanking you in advance,

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Received on Fri Jan 19 2018 - 15:30:03 PST
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